On Mon, Jul 23, 2012, Wook Lee wrote:
> I generated two crd files from two pdb files which are different from
> each other only in disappearing atom.
> However, when leap generates crd files from those pdb files, it
> exchanges the coordinates for HB2 and HB3 of cysteine residue.
> So HB2 atom of first crd file has the coordinate of HB3 atom of second
> crd file and vice versa.
Are the hydrogen atoms in the PDB files, or is LEaP creating them? (If LEaP
is trying to build them, then do this: first create a file with all hydrogens
for the full system; then edit that file (with all hydrogens), just removing
the atoms that are going to disappear.)
Do the two pdb files differ at the cysteine in question (e.g. with fewer atoms
in that side chain for one system than the other)? LEaP uses the side chain
positions to locate hydrogens, so that would explain the behavior. One fix is
described in the paragraph above; you could also just manually edit the
coordinate files to swap the coordinates of HB2 and HB3. Of course, be
careful!
...dac
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Received on Mon Jul 23 2012 - 07:00:02 PDT
